Multiple Waves of Recent DNA Transposon Activity in the Bat, Myotis Lucifugus
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Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus David A. Ray,1,5,6 Cedric Feschotte,2,5 Heidi J.T. Pagan,1 Jeremy D. Smith,1 Ellen J. Pritham,2 Peter Arensburger,3 Peter W. Atkinson,3 and Nancy L. Craig4 1Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA; 2Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA; 3Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA; 4Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and Helitron elements, two distinct groups of DNA transposons, in the lineage of the vespertilionid bat Myotis lucifugus. Here, we describe seven additional families that have also been recently active in the bat lineage. Early vespertilionid genome evolution was dominated by the activity of Helitrons, mariner-like and Tc2-like elements. This was followed by the colonization of Tc1-like elements, and by a more recent explosion of hAT-like elements. Finally, and most recently, piggyBac-like elements have amplified within the Myotis genome and our results indicate that one of these families is probably still expanding in natural populations. Together, these data suggest that there has been tremendous recent activity of various DNA transposons in the bat lineage that far exceeds those previously reported for any mammalian lineage. The diverse and recent populations of DNA transposons in genus Myotis will provide an unprecedented opportunity to study the impact of this class of elements on mammalian genome evolution and to better understand what makes some species more susceptible to invasion by genomic parasites than others. [Supplemental material is available online at www.genome.org.] Transposable elements represent a substantial fraction of many man DNA transposon families younger than ∼37 Myr (Pace and eukaryotic genomes. For example, ∼50% of the human genome is Feschotte 2007). derived from transposable element sequences (Lander et al. In stark contrast to the situation in human and mouse, there 2001). Other genomes, especially those of plants, may consist of is mounting evidence for recent and substantial DNA transposon substantially higher proportions of transposable element-derived activity in the vespertilionid bat Myotis lucifugus. In one study, DNA (SanMiguel and Bennetzen 1998; Bennetzen 2000). Trans- this conclusion was inferred from the presence of minimally di- posable elements are typically divided into two classes (Wicker et verged nonautonomous hAT transposons, the polymorphic sta- al. 2007). Class 1 is represented by the retrotransposons (LINEs, tus of some of these transposons in natural Myotis populations, SINEs, LTRs, and ERVs). Class 2 includes the “cut-and-paste” and the discovery of an apparently full-length and potentially DNA transposons, which are characterized by terminal inverted functional autonomous hAT transposon (Ray et al. 2007). In a repeats (TIRs) and are mobilized by an element-encoded trans- separate report, an extensive and recently amplified population posase. Currently, 10 superfamilies of cut-and-paste DNA trans- of Helitrons, a distinct subclass of DNA transposons, was discov- posons are recognized in eukaryotes (Feschotte and Pritham ered in the M. lucifugus genome (Pritham and Feschotte 2007). 2007). These surprising observations raised a number of intriguing ques- While class 2 elements are widespread and active in a variety tions about the activity of DNA transposons and its genomic of eukaryotes, they have been thought to be transpositionally impact in Myotis and other bats. In particular, we wondered inactive in mammalian genomes. This conclusion was based pri- whether the discovery of relatively recent hAT and Helitron ac- marily on the initial analyses of the human and mouse genome tivity in Myotis were merely coincidental or whether it reflected sequences. While both species harbor a significant number and a some unique biological or genomic features of bats in general or diverse assortment of DNA transposons, they show no signs of vespertilionids in particular that has allowed DNA transposons to recent activity (Lander et al. 2001; Waterston et al. 2002). For invade and expand in these genomes, while such occurrences example, there are more than 300,000 DNA elements recogniz- appear to be rare or nonexistent in other mammalian genomes. able in the human genome, which are grouped into 120 families As a prelude to addressing these questions we examined M. lu- and belong to five superfamilies. A large subset of these elements cifugus for additional traces of DNA transposon activity. Conse- (40 families; ∼98,000 copies) were integrated in the last 40–80 quently, we explored the diversity, abundance, and evolutionary million years (Myr), but there remains no evidence for any hu- history of DNA transposons in the M. lucifugus genome. Herein, we characterize seven new families of DNA trans- 5These authors contributed equally to this work. posons from the current whole-genome sequence of M. lucifugus. 6 Corresponding author. In addition, we provide additional information on the previously E-mail [email protected]; fax (304) 293-6363. Article published online before print. Article and publication date are at http:// described Myotis_hAT transposons (Ray et al. 2007). Together, www.genome.org/cgi/doi/10.1101/gr.071886.107. these elements represent three distinct superfamilies and exhibit 18:000–000 ©2008 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/08; www.genome.org Genome Research 1 www.genome.org Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Ray et al. clear signs of recent activity in the vespertilionid lineage, that is, Tigger-like elements called Tigger1_ML. A tentative consensus was within the last 40–50 Myr. We also identified a ninth transposon reconstructed from the alignment of the seven longest copies. lineage that likely expanded prior to the chiropteran divergence. The size (2.8 kb) and TIRs are consistent with other Tigger ele- One family represents the youngest DNA transposon family so ments and the consensus is similar to consensus sequences in far recorded in any mammalian species, one that is likely still Repbase as Tigger1a_CAR and Tigger1a_ART, which represent Tig- expanding in the genome. The discovery of this unprecedented ger1-like families specific to carnivores and artiodactyls, respec- level of DNA transposon activity in a mammalian genome rep- tively. We also identified several highly eroded copies of a related resents a dramatic shift in our view of mobile element biology in family of Tigger1 transposons in the European hedgehog, Erina- mammals. ceus europaeus (e.g., accession AANN01830819, position 1599– 4234). Given that hedgehog, carnivores, artiodactyls, and chirop- terans are all part of the well-supported Laurasiatheria super- Results order, we hypothesize that Tigger1_ML amplified during the early part of the Laurasiatherian radiation. This is by far the oldest hAT superfamily family of DNA transposons that we identified and, as it does not The consensus sequence for Myotis_hAT1 was previously de- appear to be unique to chiropterans, we have chosen not to focus scribed (Ray et al. 2007). To summarize, the entire sequence on the details of this family in the current study. spans 2921 nucleotides with a single ORF consisting of bases The Tc2 group is sister to the pogo lineage and was first 700–2631 that encodes an apparently intact transposase of 643 identified in Caenorhabditis elegans (Ruvolo et al. 1992). There are amino acids (aa). The present analysis confirms the characteristic relatively few Tc2-like elements in human, and their amplifica- target-site duplications (TSDs) for Myotis hAT elements, 8 bp with tion predates the split of eutherian mammals (Pace and Feschotte a central TA dinucleotide, and the typical short TIR (terminal 2007). In contrast, we identified a distinct and much more recent inverted repeats) sequence. Myotis_hAT1 and its nonautonomous family of Tc2-like elements in M. lucifugus. The Tc2_1_ML con- derivatives are by far the most abundant family of elements ana- sensus is 1728 bp with 23 bp TIRs similar to known or newly lyzed in this study, with >96,000 hits of Ն100 bp in the current identified Tc2 elements. It contains a single ORF spanning posi- WGS data. tions 213–1559 and encoding a putative transposase of 448 aa. We identified a second family of hAT elements, called Phylogenetic analysis confirms that Tc2_1_ML belongs to the Tc2 hAT2_ML. The TIRs of hAT2_ML are highly similar to Myotis_ group, but does not cluster with either of the mammalian Tc2- hAT1, but the internal sequence is only weakly similar. hAT2_ML like transposases identified in human (Kanga), opposum is predicted to encode a 428-aa transposase with only minimal (Tc2_MD2), and tenrec (Tc2_Et), or with the human transposase- sequence similarity and 33% amino acid identity to the Myotis_